b9b3c73197da510f27595dcf63646cabeb3ebe8c
markd
  Tue Jul 12 11:53:41 2022 -0700
add All GENCODE VM30

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index 27924dc..5f7919a 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -228,15 +228,46 @@
     pushd ~/kent/src/hg/makeDb/trackDb
     ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M30 107 'June 2022'
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include  as alpha
     jkmake DBS=mm39
 
     # edit all.joiner to add ~/tmp/gencodeVM30.joiner
 
     pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImportPre
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
 ##############################################################################
+2022-07-12: import of UCSC GENCODE group processing of GENCODE VM30 release (markd)
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/mm39/bed/gencodeVM30/hgcImport
+    pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImport
+
+    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
+
+    # compare tables from previous release to see if number changed makes
+    # sense.  Results are in gencode-cmp.tsv
+
+    # generate trackDb and joiner blurb
+    pushd ~/kent/src/hg/makeDb/trackDb
+    ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M30 107 'July 2022'
+
+    # Update 'Release Notes' in
+    # mouse/mm39/wgEncodeGencodeSuper.html
+
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
+    jkmake DBS=mm39
+
+    ## only if being pushed to RR:
+    # edit all.joiner to add ~/tmp/gencodeVM30/hgcImport.joiner
+    # verify with:
+    pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImport
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    make DBS=mm39 alpha
+##############################################################################